Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (T-m's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At T-m Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at T-m with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a P-fold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

Efeito do dentifrício fluoretado na incidência de cárie na dentição decídua e fluorose na dentição permanente: revisões sistemáticas e metanálises

Apesar do potencial anticárie do dentifrício fluoretado na dentição permanente estar bem estabelecido, existe uma lacuna no conhecimento em relação ao seu efeito na dentição decídua; não existe consenso quanto à concentração ideal de fluoreto no dentifrício capaz de maximizar o benefício anticárie na dentição decídua e simultaneamente minimizar o risco de desenvolver fluorose clinicamente importante na dentição permanente. O artigo 1 desta tese avaliou o efeito dos dentifrícios de concentração baixa (menos de 600 ppm) e padrão (1000 a 1500 ppm) de fluoreto comparados com placebo ou nenhuma intervenção e o artigo 2 comparou diretamente o efeito do dentifrício de concentração baixa de fluoreto com o de concentração padrão. Foi realizada uma revisão sistemática de ensaios clínicos randomizados ou quasi-randomizados. Dois examinadores leram, de forma independente, 1932 resumos ou citações e 159 estudos na íntegra. As discordâncias foram resolvidas por um terceiro examinador. Oito estudos foram incluídos no artigo 1 e cinco no artigo 2. Para avaliar o efeito dos dentifrícios fluoretados sobre o número de dentes e superfícies dentárias cariadas, perdidas por cárie e obturadas, e sobre o número de crianças com cárie e fluorose, foram estimados frações prevenidas (FP) e riscos relativos (RR) combinados, respectivamente. Quando os dentifrícios de concentração padrão de fluoreto foram comparados com placebo ou nenhuma intervenção, houve reduções significativas de cárie no nível de superfície (FP= 31%; IC 95% 18 43), dente (FP= 16%; IC 95% 7 24) e indivíduo (RR= 0,86; IC 95% 0,81 0,93). Quando os dentifrícios de concentração baixa de fluoreto foram comparados com nenhuma intervenção, houve redução significativa de cárie apenas no nível de superfície (FP= 40%; IC 95% 5 75) (artigo 1). Os dentifrícios de concentração baixa de fluoreto, comparados diretamente com os de concentração padrão, aumentaram significativamente o risco de cárie na dentição decídua (RR= 1,13; IC 95% 1,07 1,20) e não reduziram significativamente o risco de fluorose clinicamente importante nos dentes permanentes anteriores superiores (RR= 0,32; IC 95% 0,03 2,97). Houve uma redução significativa de cárie no nível de dente quando o dentifrício com concentração padrão de fluoreto foi comparado com o de baixa concentração (FP=14%; IC 95% 6 21). Porém, não houve diferença no nível de superfície, apesar de ter havido uma tendência favorecendo os dentifrícios com concentração padrão de fluoreto e pH neutro (FP= 13%; IC 95% -4 30) e os de concentração baixa de fluoreto e pH ácido (FP= -5%; IC 95% -22 11) (artigo 2). Os dentifrícios de concentração padrão de fluoreto foram mais efetivos na redução de cárie na dentição decídua de pré-escolares do que os de concentração baixa, placebo ou nenhuma intervenção. Os dentifrícios de concentração padrão de fluoreto, em comparação com os de concentração baixa, não aumentaram significativamente o risco de fluorose clinicamente importante nos dentes permanentes anteriores superiores. São necessários mais estudos para confirmar se a redução do pH dos dentifrícios de concentração baixa de fluoreto pode ser considerada uma alternativa para aumentar o efeito anticárie e reduzir o risco de fluorose clinicamente importante.

Improved handling and preservation of freshwater giant prawn, Macrobrachium rosenbergii for producing safe and wholesome products

Studies were undertaken to evaluate the quality changes in freshwater giant prawn, Macrobrachium rosenbergii during various storage conditions of handling and preservation and producing safe and quality products. The samples kept in ice immediately after catch with head-on and head-less condition were found to be acceptable for 6 days and 7 days, respectively. Delaying of icing considerably shortened the shelf-life. The pH value increased from 6.36 to 8.0 after 10 days in ice. The initial average TVB-N value of sample increased from below 10 mg/100 g to 25 mg/100 g with the lapse of storage period. The Ca++ ATPase activity in presence of 0.1M KCl slightly decreased at the end of 10 days of ice storage. Immediately after harvest, initial aerobic plate count (APC) was 2.88x10^6 CFU/g which gradually increased to 1.12x10^8 CFU/g after 6 days in ice storage and showed early signs of spoilage. Initial bacterial genera in the prawn iced at 0 hours were comprised of Coryneform (22.21 %), Bacillus (7.40%), Micrococcus (11.11 %), Achromobacter (48.14%), Flavobacterium/Cytophaga (7.40%), Pseudomonas (3.70%) and Aeromonas (3.70%). During ice storage Coryneforms and Bacillus were always dominating along with less prominent ones - Micrococcus, Achromobacter and Flavobacterium. Studies were conducted on the stability of myofibrillar protein of M. rosenbergii under different storage and pH conditions. The influence of a wide range of pH on the remaining Ca++ ATPase activity of M. rosenbergii muscle myofibrils after storage at -20°C for 2 days, at 0°C for 2 days and at 35°C for 30 minutes demonstrated that ATPase activities were lower in acidic and alkaline pH regions and the activity remained relatively high. Mg++ ATPase activities both in presence and absence of Ca++ remained high at neutral pH compared to those of acidic and alkaline region. The solubility of myofibrillar protein decreased gradually both in acidic and alkaline pH regions. The study also examined the bacteriological quality of freshly harvested M. rosenbergii, pond sediment and pond water from four commercial freshwater prawn farms at Fulpur and Tarakanda upazilas in the district of Mymensingh. The study included aerobic plate count (APC), total coliform count, detection, isolation and identification of suspected public health hazard bacteria and their seasonal variation, salt tolerance test, antibiotic sensitivity test of the isolates and washing effect of chlorinated water on the bacterial load in the prawn samples. APC in sediment soil and water of the farm and gill and hepatopancreas of freshly harvested prawns varied considerably among the farms and between summer and winter season. The range of coliform count in water, gill and hepatopancreas ranged between 6 - 2.8x10^2 CFU/ml, 1.2x10^2 - 3.32x10^2 CFU/g and 1.43x10^2 - 3.89 x10^3 CFU/g, respectively. No coliform was detected in pond sediment sample. Suspected health hazard bacteria isolated and identified from pond sediment, water, gill and hepatopancreas included Streptococcus, Bacillus, Escherichia coli, Klebsialla, Salmonella, Staphylococcus, Pseudomonas and Aeromonas. Bacillus, Salmonella and Staphyloccus [sic], and were found to be highly salt tolerant and capable of growing at 10% NaCl. The antibiotic discs with different concentration of antibiotics were used for the sensitivity test. The organisms were found to be most sensitive against Tetracyclin and Gentamycin.

Interfacial recognition of human prostate-specific antigen by immobilized monoclonal antibody: effects of solution conditions and surface chemistry.

The specific recognition between monoclonal antibody (anti-human prostate-specific antigen, anti-hPSA) and its antigen (human prostate-specific antigen, hPSA) has promising applications in prostate cancer diagnostics and other biosensor applications. However, because of steric constraints associated with interfacial packing and molecular orientations, the binding efficiency is often very low. In this study, spectroscopic ellipsometry and neutron reflection have been used to investigate how solution pH, salt concentration and surface chemistry affect antibody adsorption and subsequent antigen binding. The adsorbed amount of antibody was found to vary with pH and the maximum adsorption occurred between pH 5 and 6, close to the isoelectric point of the antibody. By contrast, the highest antigen binding efficiency occurred close to the neutral pH. Increasing the ionic strength reduced antibody adsorbed amount at the silica-water interface but had little effect on antigen binding. Further studies of antibody adsorption on hydrophobic C8 (octyltrimethoxysilane) surface and chemical attachment of antibody on (3-mercaptopropyl)trimethoxysilane/4-maleimidobutyric acid N-hydroxysuccinimide ester-modified surface have also been undertaken. It was found that on all surfaces studied, the antibody predominantly adopted the 'flat on' orientation, and antigen-binding capabilities were comparable. The results indicate that antibody immobilization via appropriate physical adsorption can replace elaborate interfacial molecular engineering involving complex covalent attachments.

Swelling behaviour of alginate-chitosan microcapsules prepared by external gelation or internal gelation technology

Swelling behaviour is one of the important properties for microcapsules made by hydrogels, which always affects the diffusion and release of drugs when the microcapsules are applied in drug delivery systems. In this paper, alginate-chitosan microcapsules were prepared by different technologies called external or internal gelation process respectively. With the volume swelling degree (S-w) as an index, the effect of properties of chitosan on the swelling behaviour of both microcapsules was investigated. It was demonstrated that the microcapsules with low molecular weight and high concentration of chitosan gave rise to low S-w. Considering the need of maintaining drug activity and drug loading, neutral pH and short gelation time were favorable. It was also noticed that S-w of internal gelation microcapsules was lower than that of external gelation microcapsules, which was interpreted by the structure analysis of internal or external gelation Ca-alginate beads with the aid of confocal laser scanning microscope. (C) 2004 Elsevier Ltd. All rights reserved.

Validation and in situ application of an automated dissolved nickel monitor for estuarine studies

The validation of a fully automated dissolved Ni monitor for in situ estuarine studies is presented, based on adsorptive cathodic stripping voltammetry (AdCSV). Dissolved Ni concentrations were determined following on-line filtration and UV digestion, and addition of an AdCSV ligand (dimethyl glyoxime) and pH buffer (N-2-hydroxyethylpiperazine-N′-2-ethanesulphonic acid). The technique is capable of up to six fully quantified Ni measurements per hour. The automated in situ methodology was applied successfully during two surveys on the Tamar estuary (south west Britain). The strongly varying sample matrix encountered in the estuarine system did not present analytical interferences, and each sample was quantified using internal standard additions. Up to 37 Ni measurements were performed during each survey, which involved 13 h of continuous sampling and analysis. The high resolution data from the winter and summer tidal cycle studies allowed a thorough interpretation of the biogeochemical processes in the studied estuarine system.

Preparation and Characterization of Interpenetration Polymer Network Films Based on Poly(vinyl alcohol) and Poly(acrylic acid) for Drug Delivery

A series of full interpenetrating polymer network (full-IPN) films of poly(acrylic acid) (PAA)/poly (vinyl alcohol) (PVA) were prepared by radical solution polymerization and sequential IPN technology. Attenuated total reflectance-Fourier transform infrared spectroscopy, swelling properties, mechanical properties, morphology, and glass transition temperature of the films were investigated. FTIR spectra analysis showed that new interaction hydrogen bonds between PVA and PAA were formed. Swelling property of the films in distilled water and different pH buffer solution was studied. Swelling ratio increased with increasing PAA content of IPN films in all media, and swelling ratio decreased with increasing PVA crosslink degree. Tensile strength and elongation at break related not only to the constitution of IPNs but also to the swelling ratio of IPNs.

Preparation of poly(thionine) modified screen-printed carbon electrode and its application to determine NADH in flow injection analysis system

A poly(thionine) modified screen-printed carbon electrode has been prepared by an electrooxidative polymerization of thionine in neutral phosphate buffer. The modified electrodes are found to give stable and reproducible electrocatlytic responses to NADH and exhibit good stability. Several techniques, including cyclic voltammetry, X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), have been employed to characterize the poly(thionine) film. Further, the modified screen-printed carbon electrode was found to be promising as an amperometric detector for the flow injection analysis (FIA) of NADH, typically with a dynamic range of 5-100 muM.

Role of electron transfer of quinones in hydroxylation of phenol

It was found that at neutral pH the hydroxylation reaction rate of phenol was accelerated with an increase of the amounts of 1,4-quinone (1,4-BQ), This acceleration was ascribed to the formation of semiquinone from 1,4-BQ. The semiquinone and 1,4-BQ were suggested to play a role of actual oxidant (electron transfer) in the catalytic cycle. With further reaction, most 1,4-BQ was converted into 1,4-hydroquinone (HQ) and the corresponding mechanism was proposed.

End-column amperometric detection of aesculin and aesculetin by capillary electrophoresis

Determination of aesculin (AL) and aesculetin (AT) by capillary electrophoresis with end-column amperometric detection using a 33 mu m microdisk carbon fiber electrode is described. The HDVs, the effect of pH, buffer concentration, injection voltage, injection time and separation voltage on the peak current response (i(p)) of the analytes and the number of theoretical plates (N) were studied. The method has high sensitivity and good reproducibility. Under the optimum condition - 10 mM, pH 9.00 phosphate buffer, 4 s at 9 kV injection, separation at 15 kV and +1.0 V as the detection potential - low detection limits (S/N = 3) of 0.06 and 0.3 mu M were obtained for AL and AT, respectively. The calibration curve was linear over three orders of magnitude. The relative standard deviations (n = 15) of peak current and migration time were 3.9% and 4.6%, and 0.96% and 0.75% for 15 consecutive injections of 5 mu M AL and AT, respectively. The use of this method for the separation and detection of the two compounds present in the traditional Chinese medicine and human urine samples is also reported. (C) 1999 Elsevier Science B.V. All rights reserved.

Binuclear lanthanide complexes as catalysts for the hydrolysis of double-stranded DNA

The efficient cleavage of plasmid DNA ( pCAT) by binuclear lanthanide complexes was investigated. At 37 degrees C and neutral pH, both Ho23+L and Er23+L promoted 100% conversion of supercoiled plasmid to the nicked circular form and linear form in 1 h. The corresponding saturation kinetics curve of cleavage of pCAT plasmid by binuclear lanthanide complexes showed the expected increase with catalyst concentration. (C) 1999 Elsevier Science S.A. All rights reserved.

Studies of non-covalent protein complexes by MALDI methods

Several specific non-covalent protein complexes were successfully observed by matrix assisted desorption ionization mass spectrometry(MALDI MS). The methods described in this paper include the matrixes use of sinapinic acid(SA) and 6-aza-2-thiothymine (ATT) in neutral pH solution, as well as the improvement of two-layer sample preparation method to achieve a high sensitivity detection of stable non-covalent complexes, Myoglobin-heme complex was found simultaneously with the sinapinic acid matrix in the various pH solution(pH=2 or pH=5), The RNase S complex showed a striking intensity at the first shot, which was decreased with more laser shots. Most importantly, the observation of specific non-covalent complex in the brome mosaic virus(BMV) coat proteins would open up a new possibility to investigate the assembly and disassembly of viral capsids.

RAPID-DETERMINATION OF KINETIC-PARAMETERS FOR THE ELECTROCATALYTIC REDUCTION OF DIOXYGEN BY VITAMIN-B12 ADSORBED ON GLASSY-CARBON ELECTRODE

In this paper, the electrochemical behavior of vitamin B-12, ie cyanocobalamin (abbr. VB12) in a weak acidic aqueous solution and adsorbed on glassy carbon (GC) surface (abbr. VB12(ad)/GC) in different pH buffer solutions have been described by using cyclic voltammetry (cv). It is found that VB12 and VB12(ad)/GC exhibit catalytic activity for the electroreduction of O2 according to two reduction peaks at -0.50 and -1.00 V vs. sce; but their electrocatalytic activity is very unstable. Based on the method of hydrodynamic amperometry [B. Miller and S. Bruckenstein, J. electrochem. Soc. 117, 1033 (1970)], some kinetic parameters for the electrocatalytic reduction of O2 by VB12(ad)/GC have been determined rapidly by using a linear rotation-scan method [Rongzhong Jiang and Shaojun Dong, Electrochim. Acta 35, 1451 (1990)]. These kinetic parameters indicate that the reduction of O2 on VB12(ad)/GC gives water predominantly in both potential ranges which correspond to those two reduction peaks. Possible reaction mechanisms have been suggested.

Analysis for Flavonoids in Bee Pollens by Capillary Electrophoresis

A capillary electrophoresis (CE) method has been developed for the determination of six bioactive flavonoids that are commonly found in health foods: hesperidin, hyperin, isorhamnetin, kaempferol, quercetin and rutin. The effects of several parameters, such as pH, buffer concentration, separation voltage and UV detector wavelength, were investigated to find the optimal conditions. Using a HbBCh-NaiB-iO? buffer (pH 9.2), the analytes can be separated within 8 min. The relative standard deviations of migration times in eight injections were between 0.77% and 0.93%, and those of the peak areas ranged from 3.8% to 8.6%. A high reproducibility and excellent linearity was observed over two orders of magnitude, with detection limits (S/N = 3) ranging from 0.34ug ml to 2.9ug ml for all the six analytes. Recoveries ranged from 80.4 % to 113.9 %. The new method is simple, reproducible and sensitive. No solid phase extraction for sample pretreatment is necessary. Analysis results are accurate in application to bee pollens.